fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
threshold_parameters.hpp
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1// --------------------------------------------------------------------------------------------------
2// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3// Copyright (c) 2016-2022, Knut Reinert & MPI für molekulare Genetik
4// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
6// --------------------------------------------------------------------------------------------------
7
8#pragma once
9
10#include <filesystem>
11
12#include <seqan3/search/kmer_index/shape.hpp>
13
14namespace raptor::threshold
15{
16
18{
19 // Basic.
20 uint32_t window_size{};
21 seqan3::shape shape{};
22 uint64_t pattern_size{};
23
24 // Threshold.
25 uint8_t errors{}; // threshold_kinds::(probabilistic|lemma)
26 double percentage{std::numeric_limits<double>::quiet_NaN()}; // threshold_kinds::percentage
27 double p_max{}; // threshold_kinds::probabilistic
28 double fpr{}; // threshold_kinds::probabilistic
29 double tau{}; // threshold_kinds::probabilistic
30
31 // Cache results.
33 std::filesystem::path output_directory{};
34};
35
36} // namespace raptor::threshold
Definition: forward_strand_minimiser.hpp:19
Definition: search_arguments.hpp:22
Definition: threshold_parameters.hpp:18
double tau
Definition: threshold_parameters.hpp:29
std::filesystem::path output_directory
Definition: threshold_parameters.hpp:33
uint32_t window_size
Definition: threshold_parameters.hpp:20
double percentage
Definition: threshold_parameters.hpp:26
double fpr
Definition: threshold_parameters.hpp:28
uint8_t errors
Definition: threshold_parameters.hpp:25
double p_max
Definition: threshold_parameters.hpp:27
bool cache_thresholds
Definition: threshold_parameters.hpp:32
seqan3::shape shape
Definition: threshold_parameters.hpp:21